[Chimera-users] How to show the electron density of just selected residues? Thanks

[Pingyang Liu]

Hi Elaine,

Thanks a lot.

Best,
Andy

On Fri, Mar 2, 2012 at 3:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Andy,
> You would select the residues, then as described in the tutorial, choose
> Features... Zone from the menu of the Volume Viewer dialog and click the
> Zone button that appears within the dialog.  Make sure you have
> successfully selected something first (for example, the magnifying glass at
> the bottom right corner of the Chimera window should turn green), then
> click the Zone button, and move the slider to change the size of the zone.
>
> I assume you are referring to the "Density Display" tutorial:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html>
>
> Now about "convexity," maybe you are looking at the attributes tutorial,
> part 2:
> <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2
> >
>
> It is simply a geometric description of the surface shape. In some cases,
> people might use it to highlight the most exposed areas (high convexity is
> where the protein "sticks out") or possible binding pockets (low convexity
> = high concavity, where there are indentations in the protein).  However,
> in this tutorial, it is mainly just an example of how you can use the
> Attribute Calculator to make new attributes out of existing ones.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Mar 2, 2012, at 11:58 AM, Pingyang Liu wrote:
>
> > Hi,
> >
> > How to show the electron density of just selected residues? Thanks
> >
> > I followed the Chimera tutorial, but still the electron density of the
> whole protein was displayed.
> >
> > Another question: what does the convexity of a protein structure tell? I
> did not find much information about convexity online.
> >
> > Thanks a lot.
> >
> > Best,
> > Andy
> >
> > --
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>


-- 
Pingyang

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